CODEWITHSUNDEEP
rmulticoreknitrfifomclapply
Pepin_the_sleepy
Pepin_the_sleepy

Reputation: 297

Knitr: redirect chunk code output to terminal

I want to monitor some pretty lengthy parallelized computations embedded in a knitr file.

The computations rely on a package I have written, and the relevant function uses mclapply from the multicore package for parallelization. This function outputs progress bars to monitor the progress of the computations using a slightly modified implementation of txtProgressBar from the utils package. The progress bar is printed to the terminal and updated through a fifo connection every time an iteration of mclapply is complete.

This works fine when sourcing from a file or calling directly the function, but I find no way to get this to work within knitr. I have tried the relevant chunk options, I can get messages and warnings redirected to the terminal, but not the progress bar. Can anyone help?

Sorry for not providing a minimal working example but I don't see how I could make one in this setting.

Upvotes: 10

Views: 1329

Answers (2)

konstunn
konstunn

Reputation: 355

Having read the point about printing progress bar to stderr in Yihui's answer I would suggest temporary redirecting stdout to stderr with sink().

sink(stderr())

your_code()

sink()

Upvotes: 1

Yihui Xie
Yihui Xie

Reputation: 30194

Because txtProgressBar() writes to stdout, and knitr captures everything in stdout, so currently it is not easy to show your progress bar if it is text-based and writes to stdout. Perhaps I can use evaluate::evaluate(debug = TRUE) internally to achieve what you want, but I'm not entirely sure if that works well with the text progress bar.

My suggestions at the moment are:

  • use a GUI-based progress bar like tcltk::tkProgressBar()

  • write the progress to other places, e.g. (ab)using stderr

    ```{r progress}
pb = txtProgressBar(min = 0, max = 100, file = stderr())
for (i in 1:100) {
  setTxtProgressBar(pb, i)
  Sys.sleep(0.05)
}
close(pb)
```

  • or use your function outside a code chunk, e.g. in an inline expression (such as \Sexpr{my_multicore_function()} in Rnw or `r my_cool_fun()` in Rmd), because inline evaluation does not capture stdout

Upvotes: 8

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